similar to: R-devel_2015-09-14 throws an error in reg-packages test

I am trying to build the latest version of R (3.6.2) on a CentOS system running 7.7.1908. I have been able to build previous versions of R up to and including 3.5.3 successfully. Starting with 3.6.0 the "make check" step fails with errors relating to "pdflatex" being missing. So, I installed texlive-latex (and the 100 other rpm dependencies) then tried rebuilding R.

Hello, I'm trying to install R from sources on two Linux machines (both with Suse 12.2): 1. > uname -a Linux cs-wsok 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux 2. > uname -a Linux csltok.swansea.ac.uk 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux I am trying version

I am only reporting this because it is the current release branch and not devel. R-2.13 from svn revision 55957 builds fine, but fails make check. This happened with a fresh svn checkout 12 hours ago and it still happens as of now. Two days ago I could build R-2.13 and it passed make check on the same system, so I doubt it is a system problem. But just in case my system details are a fresh

On Wed, Sep 16, 2015 at 9:32 PM, Avraham Adler <avraham.adler at gmail.com> wrote: > When running make check, I get the following error: > > running code in 'reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1 > make[2]: *** [test-Reg] Error 2 > make[1]: *** [test-all-basics] Error 1 > make: *** [check] Error 2 > > Looking at reg-packages.Rout.fail

Testing for an NFS effect on the failure of 'make check': Try first on /usr/local/ 9:42 cd /usr/local/src/ 9:42 sudo mkdir R 9:43 sudo chown mdalphin:mdalphin R 9:43 cd R 9:43 gunzip -c /opt/apps/x86_64/R/Archive/R-3.2.5.tar.gz | tar xf - 9:43 cd R-3.2.5/ 9:44 ./configure --prefix=/opt/apps/x86_64/R/R-3.2.5 LIBnn=lib 9:44 make 9:57 make check

Hi, Let me justify building R from source. While I can obtain R built for me under Ubuntu, I tend to build it from scratch as we use a NFS-shared build as well as shared R libraries for all the bioinfo staff at this company. Only one build and one set of packages to ensure uniformity across all workstations. My problem is that despite using a pretty standard build process, I am failing at the

On Wed, Mar 11, 2015 at 1:40 AM, Hsiu-Khuern Tang <tangoh at gmail.com> wrote: > On Tue, Mar 10, 2015 at 8:54 PM, Avraham Adler <avraham.adler at gmail.com> wrote: >> >> I successfully rebuilt R-devel_2015-03-09 with the most recent version >> of Rtools tonight, building both ICU_531 and this time libcurl (7.39) >> as well (and OpenBLAS, of course). The

On Tue, Mar 10, 2015 at 3:17 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > > That's a bug. I haven't tracked down what's going wrong with our > regular code. If I can't find that and fix it soon, I'll make Internet2 > the default. For now, you can do it yourself using the instructions on > ?setInternet2. > > Duncan Murdoch I

Good evening. Testing the most recent version of Rtools, the build stops about when text.c is being compiled in the tools package (just after R.Lapack). The compilation is looking for gcc in C:, even though RTOOLS is set for another drive, and the compilation has successfully run until this point. This did not happen last night with version 1955. I've uninstalled and reinstalled Rtools three

On Wed, Mar 11, 2015 at 1:23 PM, Hsiu-Khuern Tang <tangoh at gmail.com> wrote: > On Tue, Mar 10, 2015 at 10:47 PM, Avraham Adler <avraham.adler at gmail.com> wrote: >> On Wed, Mar 11, 2015 at 1:40 AM, Hsiu-Khuern Tang <tangoh at gmail.com> wrote: >>> On Tue, Mar 10, 2015 at 8:54 PM, Avraham Adler <avraham.adler at gmail.com> wrote: >>>>

Hi, not sure this is a bug or just an unavoidable undesirable side-effect -- or just me that does not do the right thing. Consider the code and output below. It creates 2 packages: * pkgA * pkgB that creates a method for a generic defined in pkgA Changes in a method for the generic in pkgA (after re-installing pkgA) are not reflected in pkgB, unless pkgB is re-installed against the new

I was wondering: are the downstream dependencies of a package rebuilt when a package is updated on CRAN? (I'm referring to the binary packages, of course.) The reason I ask is because there are cases where this can cause problems. Suppose that when pkgB is built, it calls pkgA::makeClosure(), which returns a closure that refers to a function in pkgA. Suppose this code is in pkgA 1.0:

Hi, SETUP: Consider three packages PkgA, PkgB and PkgC. PkgA defines a generic function foo() and exports it; export(foo) PkgB imports PkgA::foo() and re-exports it; importFrom(PkgA, foo) export(foo) PkgC imports everything from PkgA and PkgB: imports(PkgA, PkgB) PROBLEM: Loading or attaching the namespace of PkgC will generate a warning: replacing previous import by

On Tue, Sep 1, 2015 at 10:57 AM, peter dalgaard <pdalgd at gmail.com> wrote: > > On 01 Sep 2015, at 16:21 , Avraham Adler <avraham.adler at gmail.com> wrote: > >> Hello. >> >> There used to be changelog of sorts for R-devel [1] and R-release [2]. >> Neither have been updated since 2015-07-24. Have these moved >> elsewhere, or are they no longer

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and exporting a generic in the namespace will also export its methods. and Note that importMethodsFrom will also import any generics defined in

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would

Hi, This strange warning happen sometimes when running 'R CMD check': * checking whether the package can be loaded with stated dependencies ... WARNING Error : .onLoad failed in loadNamespace() for ?pkgB?, details: call: length(new("A")) error: could not find function "loadMethod" Error: package/namespace load failed for ?pkgB? Execution halted

Hi, I'd like to list all package PkgA functions that another package PkgB use via Depends or Imports (ignoring Suggests for simplicity). As long as PkgB uses importFrom("PkgA", ...) it's just a matter of parsing the NAMESPACE file or inspecting asNamespace("PkgB")$.__NAMESPACE__.$imports. However, what can be done in case PkgB uses import("PkgA")? Is there

pkgA's NAMESPACE has importFrom(graphics, plot) exportClasses("A") exportMethods("plot") R/foo.R has setClass("A") setMethod("plot", "A", function(x, y, ...) {}) During R CMD INSTALL pkgA_1.0.tar.gz we are told ** preparing package for lazy loading Creating a generic function for 'plot' from package

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)